diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java b/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
index 3720a15cafe134f661fc1b06283f41292e2f9546..7794f12ee8b40c846ca82ac3fb96fc0a7be69933 100644
--- a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
+++ b/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterGetImage.java
@@ -38,11 +38,11 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
super();
importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- series = new VarInteger("Series", 0);
+ series = new VarInteger("Series", -1);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
- zIndex = new VarInteger("Z (slice) index", 0);
- tIndex = new VarInteger("T (frame) index", 0);
+ zIndex = new VarInteger("Z (slice) index", -1);
+ tIndex = new VarInteger("T (frame) index", -1);
cIndex = new VarInteger("C (channel) index", -1);
image = new Var<IcyBufferedImage>("Image", IcyBufferedImage.class);
@@ -71,7 +71,7 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
- // default values ? use internal position if any defined
+ // undefined values ? use internal position if any defined
if ((s == 0) && (pi.s != -1))
s = pi.s;
if ((z == 0) && (pi.z != -1))
@@ -83,6 +83,10 @@ public class SequenceFileImporterGetImage extends Plugin implements IOBlock, Plu
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
+ // still undefined ? --> set default value for series
+ if (s == -1)
+ s = 0;
+
try
{
image.setValue(imp.getImage(s, res, rect, z, t, c));
diff --git a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java b/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
index 34c8ba2d6a387750d1b97aef4b1300a5f8c6dda8..666f65cc710b68cabe97b37fd1ecaaf4b2c604b5 100644
--- a/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
+++ b/src/plugins/tprovoost/sequenceblocks/importer/SequenceFileImporterLoadSequence.java
@@ -43,7 +43,7 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
importer = new Var<PositionedSequenceFileImporter>("Importer", PositionedSequenceFileImporter.class);
- series = new VarInteger("Series", 0);
+ series = new VarInteger("Series", -1);
resolution = new VarInteger("Resolution (0=full, 1=1/2, ..)", 0);
region = new VarROIArray("XY region (ROI)", null);
minZIndex = new VarInteger("Z min (slice)", -1);
@@ -80,8 +80,8 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
Rectangle rect = ((rois != null) && (rois.length > 0)) ? rois[0].getBounds5D().toRectangle2D().getBounds()
: null;
- // default values ? use internal position if any defined
- if ((s == 0) && (pi.s != -1))
+ // undefined values ? use internal position if any defined
+ if ((s == -1) && (pi.s != -1))
s = pi.s;
if ((minZ == -1) && (maxZ == -1) && (pi.z != -1))
{
@@ -93,10 +93,14 @@ public class SequenceFileImporterLoadSequence extends Plugin implements IOBlock,
minT = pi.t;
maxT = pi.t;
}
- if ((c == 0) && (pi.c != -1))
+ if ((c == -1) && (pi.c != -1))
c = pi.c;
if ((rect == null) && (pi.xyRegion != null))
rect = pi.xyRegion;
+
+ // still undefined ? --> set default value for series
+ if (s == -1)
+ s = 0;
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
index 782c76cf22a1fcc65214f96af01bd64148f79d4c..134d9af71ed8971b8503e86dc944698a857de19c 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterBatch.java
@@ -1,11 +1,15 @@
package plugins.tprovoost.sequenceblocks.loop;
+import java.util.List;
+
import icy.file.SequenceFileImporter;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import plugins.adufour.blocks.lang.Batch;
import plugins.adufour.blocks.tools.sequence.SequenceBlock;
+import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarInteger;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.SequenceBlocks;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -18,11 +22,21 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
public abstract class SequenceFileImporterBatch extends Batch implements SequenceBlock, PluginLibrary, PluginBundled
{
// important to not initialize and create them in getBatchSource() and getBatchElement()
- protected Var<PositionedSequenceFileImporter> positionedImporter;
- protected Var<PositionedSequenceFileImporter> element;
+ protected Var<PositionedSequenceFileImporter> positionedImporter = null;
+ protected Var<PositionedSequenceFileImporter> element = null;
+ protected VarInteger series = null;
// internal
protected int limit;
+ protected boolean showSeriesField;
+
+ public SequenceFileImporterBatch()
+ {
+ super();
+
+ // we want it by default
+ showSeriesField = true;
+ }
@Override
public Var<PositionedSequenceFileImporter> getBatchSource()
@@ -58,8 +72,52 @@ public abstract class SequenceFileImporterBatch extends Batch implements Sequenc
if (imp.getOpened() == null)
throw new VarException(positionedImporter, "Importer is not opened !");
- // init element with a copy of current positioned importer
- element.setValue(new PositionedSequenceFileImporter(value));
+ // create new positioned importer for element initialization
+ final PositionedSequenceFileImporter pi = new PositionedSequenceFileImporter(value);
+
+ // series field active ?
+ if (showSeriesField)
+ {
+ final int s = series.getValue().intValue();
+
+ // defined series ? --> set series position
+ if (s != -1)
+ pi.s = s;
+ }
+
+ // init element with a copy of current positioned importer (and eventually set serie position)
+ element.setValue(pi);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ if (showSeriesField)
+ {
+ // lazy creation
+ if (series == null)
+ series = new VarInteger("Series", -1);
+
+ inputMap.add("series", series);
+ }
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ if (showSeriesField)
+ {
+ // lazy creation
+ if (series == null)
+ series = new VarInteger("Series", -1);
+
+ loopVariables.add(series);
+ }
+
+ // need to be called after
+ super.declareLoopVariables(loopVariables);
}
@Override
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
index 46640c56371c0c1eade6faae2c6d3a23d531ce35..afc3b0405731be0aab4532d1fec43677f797bbe9 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterChannelBatch.java
@@ -17,7 +17,8 @@ public class SequenceFileImporterChannelBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
index e91d5f4ff98aba478bb7aa82b97957726f288141..ba8bf1066324d59de57918deaf474eb654dae72b 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterFrameBatch.java
@@ -17,7 +17,8 @@ public class SequenceFileImporterFrameBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
index 0bbd8bb263a02730c16eb1c2aa4fac2fd7dad8cd..98ab352ebf2a023456d4109e83fe45150b073fc6 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterRegionBatch.java
@@ -24,9 +24,9 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
{
- protected VarROIArray rois;
- protected VarInteger inputRoisResolution;
- protected VarInteger inputRoisMargin;
+ protected VarROIArray rois = null;
+ protected VarInteger inputRoisResolution = null;
+ protected VarInteger inputRoisMargin = null;
protected List<Rectangle> regions;
@Override
@@ -34,7 +34,8 @@ public class SequenceFileImporterRegionBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
// can iterate over XY dimension ?
if ((pi.xyRegion == null) && (rois.getValue() != null))
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
index 255c14ceb98dbccc3ec8b09e5a4db47f420a240f..c08970f3bfc25a3dabeae22bd5489de1ab988f26 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSeriesBatch.java
@@ -12,17 +12,29 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
{
+ public SequenceFileImporterSeriesBatch()
+ {
+ super();
+
+ // add series field here
+ showSeriesField = false;
+ }
+
@Override
public void initializeLoop()
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
- // force series iteration as by default series is set to 0
- limit = MetaDataUtil.getNumSeries(pi.getMetadata());
+ // can iterate over S dimension ?
+ if (pi.s == -1)
+ limit = MetaDataUtil.getNumSeries(pi.getMetadata());
+ else
+ limit = 1;
}
catch (Exception e)
{
@@ -35,9 +47,12 @@ public class SequenceFileImporterSeriesBatch extends SequenceFileImporterBatch
public void beforeIteration()
{
// set current position S
- element.getValue().s = getIterationCounter().getValue().intValue();
- // force element changed event so loop get correctly executed
- element.valueChanged(element, element.getValue(), element.getValue());
+ if (positionedImporter.getValue().s == -1)
+ {
+ element.getValue().s = getIterationCounter().getValue().intValue();
+ // force element changed event so loop get correctly executed
+ element.valueChanged(element, element.getValue(), element.getValue());
+ }
}
@Override
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
index 061b76de2ce25f577b22617ab6d0e5ec2b1049a7..93a5514285f7563ec343e5d173322757dc65f535 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterSliceBatch.java
@@ -17,7 +17,8 @@ public class SequenceFileImporterSliceBatch extends SequenceFileImporterBatch
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
try
{
diff --git a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
index 5386fb6de960654e2274d0f96aebebc51482b1a6..b831e80c1a090fc5333e150300b372bf4caf1827 100644
--- a/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
+++ b/src/plugins/tprovoost/sequenceblocks/loop/SequenceFileImporterTileBatch.java
@@ -6,7 +6,10 @@ import java.util.List;
import icy.file.SequenceFileImporter;
import icy.image.ImageUtil;
import icy.sequence.MetaDataUtil;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.util.VarException;
import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
@@ -17,25 +20,18 @@ import plugins.tprovoost.sequenceblocks.importer.PositionedSequenceFileImporter;
*/
public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
{
- protected final VarInteger tileW;
- protected final VarInteger tileH;
+ protected VarInteger tileW;
+ protected VarInteger tileH;
protected List<Rectangle> tiles;
- public SequenceFileImporterTileBatch()
- {
- super();
-
- tileW = new VarInteger("Tile width (-1 = auto)", 0);
- tileH = new VarInteger("Tile height (-1 = auto)", 0);
- }
-
@Override
public void initializeLoop()
{
super.initializeLoop();
- final PositionedSequenceFileImporter pi = positionedImporter.getValue();
+ // can take position from element which should have been initialized here
+ final PositionedSequenceFileImporter pi = element.getValue();
// can iterate over XY dimension ?
if (pi.xyRegion == null)
@@ -63,7 +59,7 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
}
catch (Exception e)
{
- throw new VarException(positionedImporter,
+ throw new VarException(element,
"Error while initializing SequenceFileImporter tile batch: " + e.getMessage());
}
@@ -88,6 +84,37 @@ public class SequenceFileImporterTileBatch extends SequenceFileImporterBatch
else
limit = 1;
}
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ // lazy creation
+ if (tileW == null)
+ tileW = new VarInteger("Tile width (-1 = auto)", 0);
+ if (tileH == null)
+ tileH = new VarInteger("Tile height (-1 = auto)", 0);
+
+ inputMap.add("tileWidht", tileW);
+ inputMap.add("tileHeight", tileH);
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ // lazy creation
+ if (tileW == null)
+ tileW = new VarInteger("Tile width (-1 = auto)", 0);
+ if (tileH == null)
+ tileH = new VarInteger("Tile height (-1 = auto)", 0);
+
+ loopVariables.add(tileW);
+ loopVariables.add(tileH);
+
+ // need to be called after
+ super.declareLoopVariables(loopVariables);
+ }
@Override
public void beforeIteration()